The game begins on July 24, 1998 after Alpha team locates Bravo team's helicopter, but there are no signs of survivors; only the corpse of Kevin Dooley, the pilot, is found. While searching the area for further clues, Alpha team is attacked by ferocious dogs, who kill one of the team's members, Joseph Frost. Alpha's helicopter pilot, Brad Vickers, panics and takes off alone. Pursued by the dogs who killed their colleague, Alpha team is forced to seek refuge within a nearby mansion. It is believed to be abandoned.
With the dogs roaming outside, the four remaining Alpha team members (Albert Wesker; Chris Redfield; Barry Burton and Jill Valentine) are trapped within. A gunshot rings out, and Barry and Jill are ordered to investigate. Upon reaching a dining room, Barry discovers a patch of human blood on the floor by the fireplace.
Jill exits the room to continue the investigation, almost immediately finding the source of the gunshot. On the floor lies S.T.A.R.S. Bravo team member Kenneth J. Sullivan, with his neck being torn out and consumed by another man. The man notices Jill's presence and turns around, revealing him to be grotesquely deformed. Jill runs back to the Dining room to warn Barry, who shoots and kills the approaching zombie. After discovering that Chris and Wesker have disappeared, Barry hands Jill a lockpick to help her around the mansion before leaving to pursue his own investigation.
Meanwhile, Chris stumbles onto his dear friend and marksmanship rival of Bravo team, Forest Speyer. Initially appearing dead and covered in blood, he re-awakens as a zombie and makes his way towards Chris, intent on devouring his flesh. Chris kills him to allow him to finally rest in peace. Leaving Forest's body outside, Chris opens a door on the west-wing of the mansion to discover Bravo team member Richard Aiken, who is laying down injured and being nursed by a woman who introduces herself as the team's new recruit, Rebecca Chambers. Rebecca informs Chris of the situation - Richard has been bitten by a poisonous snake and needs the serum or he will die from the toxin. Not wanting another friend to die, Chris obliges and tracks down the serum, handing it over in time to allow Richard's survival.
Elsewhere, Jill finds a shotgun in a lounge area, but does not realize until it is too late that its removal has triggered a booby trapped ceiling to collapse on the room, albeit slowly. Luckily, Barry breaks down the door to let her out just in time. In a bar on the east-wing, Jill finds a piano; recovering part of a piano sheet, she plays "Moonlight Sonata", which she recognizes. A secret compartment in the room opens up and she uncovers the tale of a man imprisoned by a "Sir Spencer". She then heads upstairs into the attic, where she confronts and defeats the giant snake that had attacked Aiken (though she is unaware of this), which escapes through a hole in the wall.
Underneath a small cemetery, Chris places four masks onto ornaments as per the "Book of Curse" he has found. It triggers the release of a crimson-colored zombie, which is much more powerful than other zombies. Chris continues to fire at the man until he finally falls to the ground, dead. Heading off to the courtyard, Richard's radio picks up a weak message from Wesker, warning any listeners of a "monster in chains".
Jill, meanwhile, explores the staff dormitory on the other end of the courtyard. Walking past room 002, she overhears Barry talking to an unknown person. Barry, who is actually being told by Captain Wesker about his apparent mission to destroy the S.T.A.R.S. team, is clearly worried. After Wesker leaves through a hidden ladder, Jill enters the room and, believing Barry to be talking to himself, becomes worried for him. Eventually making it into the underground aqua ring, Jill pours the V-JOLT chemical onto PLANT 42's routes as instructed in a file. Heading up to Point 42 where the plant was growing, Jill is surprised to discover that the monster is able to survive the poison, and even more so when its roots grab hold of her and lift her above the ground. Barry suddenly barges in through the door unexpectedly with a flamethrower, killing the plant once and for all.
Chris returns from Lisa's cabin to find the mansion home to a number of the newly-released Hunter α. He wanders the mansion and eventually ends up in the library, where he is attacked by the giant snake again, and kills it. After exploring Spencer's office, he overhears Rebecca screaming upstairs. Racing towards the upstairs lounge, he stops another hunter from killing her just in time - it had already cornered her when he killed it.
Jill, exploring the spider-filled underground caves, discovers an injured Enrico Marini sitting on the floor. He warns her that there was a traitor within the S.T.A.R.S. unit, planted by Umbrella to betray them if the time called for it. Before he can divulge on who exactly he discovered the traitor to be, he is assassinated by an unseen assailant.
Leaving the mansion for the caves not far behind Jill, Chris gains access to an elevator to a lower cave-system. Encountering Lisa Trevor again, Chris instead uses the cave system to his advantage and avoids a direct confrontation altogether. Climbing up a ladder, he finds himself in the very cottage he first met Lisa in, recovering files explaining her sad history in the process. Returning to the mansion's Main Hall, Chris fits in two hexagonal-pieces into holes behind the staircase to unlock a gate to the underground. Heading downstairs, he makes it into a series of labs below the mansion.
Jill, following that same trail, stumbles onto Barry again. He pulls his gun on her but is disarmed. They are then attacked by none other than Lisa Trevor. With Barry providing a distraction, Jill manages to open up a sarcophagus, revealing the corpse of Jessica Trevor to her daughter, who promptly throws herself down a chasm into the pitch-black beyond.
With both Chris and Jill reaching the underground laboratory complex, they continue their investigation, knowing full well that the Umbrella Corporation is heavily-involved in the events. Searching through surviving data, Chris, during his search, meets Rebecca again, who has been trying to catch up with him for a while. Jill discovers which one of their number was an Umbrella employee assigned to the facility - Albert Wesker. Filled with rage, she attempts to track him down in the lower levels, and is surprised to be held at gunpoint by Barry, who, despite her earlier suspicions, she had already denounced as the traitor Enrico had warned her about. Taking her to the adjacent room, she is greeted by Wesker, who explains how he forced Barry into doing his bidding by having his family taken hostage, before introducing her to one more thing: Tyrant. Attempting to activate it, he explains that he has programmed it to hunt down the surviving S.T.A.R.S. officers, Jill included. Wesker however, cannot wait and raises his handgun at her, only to be shot by Barry. Apologizing to Jill for the trouble he caused her, he does not notice Wesker finishing the Tyrant activation process until it is too late. The creature awakes from its slumber and burst from its capsule, heading straight for Barry before changing its mind and killing Wesker first. After a short fight, Jill renders the Tyrant unconscious, and the two quickly leave the room.
Soon after, they meet up with Chris and Rebecca(who have figured out that Wesker betrayed them), the latter of whom leaves to activate the facility's self-destruct system before retreating. Receiving another message from Brad, who stresses that he is low on fuel and would be leaving soon, Chris, Jill and Barry make their way to the helipad outside to get his attention. They fire a flare into the air as a signal, Brad arrives to pick them up, but is stopped from doing so after the Tyrant bursts through the floor of the helipad. Rebecca, meanwhile, after activating the self-destruct, makes it to the helipad and meets up with them in time to see the Tyrant break loose. After a short fight, Brad gains the courage to help, knocking a rocket launcher out of the side of the helicopter. With its sights on the Tyrant, a rocket shoots out and disintegrates the monster then and there.
Free to land, Brad picks up the four and takes them back to the safety of Raccoon City.